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Class: SmallMolecule

A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion).

URI: biolink:SmallMolecule

classDiagram class SmallMolecule MolecularEntity <|-- SmallMolecule SmallMolecule : available_from SmallMolecule --|> DrugAvailabilityEnum : available_from SmallMolecule : category SmallMolecule : description SmallMolecule : full_name SmallMolecule : has_attribute SmallMolecule --|> attribute : has_attribute SmallMolecule : has_chemical_role SmallMolecule --|> chemical role : has_chemical_role SmallMolecule : id SmallMolecule : iri SmallMolecule : is_metabolite SmallMolecule : is_toxic SmallMolecule : max_tolerated_dose SmallMolecule : name SmallMolecule : provided_by SmallMolecule : synonym SmallMolecule : trade_name SmallMolecule --|> chemical entity : trade_name SmallMolecule : type SmallMolecule : xref

Inheritance

Slots

Name Cardinality and Range Description Inheritance
is_metabolite 0..1
Boolean		 indicates whether a molecular entity is a metabolite MolecularEntity
trade_name 0..1
ChemicalEntity		 ChemicalEntity
available_from 0..*
DrugAvailabilityEnum		 ChemicalEntity
max_tolerated_dose 0..1
String		 The highest dose of a drug or treatment that does not cause unacceptable side... ChemicalEntity
is_toxic 0..1
Boolean		 ChemicalEntity
has_chemical_role 0..*
ChemicalRole		 A role is particular behaviour which a chemical entity may exhibit ChemicalEntity
provided_by 0..*
String		 The value in this node property represents the knowledge provider that create... NamedThing
xref 0..*
Uriorcurie		 A database cross reference or alternative identifier for a NamedThing or edge... NamedThing
full_name 0..1
LabelType		 a long-form human readable name for a thing NamedThing
synonym 0..*
LabelType		 Alternate human-readable names for a thing NamedThing
id 1..1
String		 A unique identifier for an entity Entity
iri 0..1
IriType		 An IRI for an entity Entity
category 1..*
CategoryType		 Name of the high level ontology class in which this entity is categorized Entity
type 0..*
String		 Entity
name 0..1
LabelType		 A human-readable name for an attribute or entity Entity
description 0..1
NarrativeText		 a human-readable description of an entity Entity
has_attribute 0..*
Attribute		 connects any entity to an attribute Entity

Aliases

  • chemical substance

Identifier and Mapping Information

Valid ID Prefixes

Instances of this class should have identifiers with one of the following prefixes:

  • CHEBI

  • PUBCHEM.COMPOUND

  • CHEMBL.COMPOUND

  • UNII

  • DRUGBANK

  • MESH

  • CAS

  • DrugCentral

  • GTOPDB

  • HMDB

  • KEGG.COMPOUND

  • ChemBank

  • PUBCHEM.SUBSTANCE

  • SIDER.DRUG

  • INCHI

  • INCHIKEY

  • KEGG.GLYCAN

  • KEGG.DRUG

  • KEGG.ENVIRON

  • KEGG

  • BIGG.METABOLITE

  • UMLS

  • foodb.compound

Schema Source

  • from schema: https://w3id.org/biolink/biolink-model

Mappings

Mapping Type Mapped Value
self biolink:SmallMolecule
native biolink:SmallMolecule
narrow STY:T196, CHEBI:59999, bioschemas:ChemicalSubstance, STY:T123, STY:T131, STY:T125, STY:T197, STY:T109, STY:T118, STY:T111, STY:T119, STY:T124, STY:T115, STY:T110, STY:T127

LinkML Source

Direct

name: small molecule
id_prefixes:
- CHEBI
- PUBCHEM.COMPOUND
- CHEMBL.COMPOUND
- UNII
- DRUGBANK
- MESH
- CAS
- DrugCentral
- GTOPDB
- HMDB
- KEGG.COMPOUND
- ChemBank
- PUBCHEM.SUBSTANCE
- SIDER.DRUG
- INCHI
- INCHIKEY
- KEGG.GLYCAN
- KEGG.DRUG
- KEGG.ENVIRON
- KEGG
- BIGG.METABOLITE
- UMLS
- foodb.compound
description: A small molecule entity is a molecular entity characterized by availability
  in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation
  of its precise chemical structure; for convenience of representation, any valid
  chemical representation is included, even if it is not strictly molecular (e.g.,
  sodium ion).
in_subset:
- model_organism_database
- translator_minimal
from_schema: https://w3id.org/biolink/biolink-model
aliases:
- chemical substance
narrow_mappings:
- STY:T196
- CHEBI:59999
- bioschemas:ChemicalSubstance
- STY:T123
- STY:T131
- STY:T125
- STY:T197
- STY:T109
- STY:T118
- STY:T111
- STY:T119
- STY:T124
- STY:T115
- STY:T110
- STY:T127
is_a: molecular entity
slot_usage:
  id:
    name: id
    examples:
    - value: CHEBI:29101
      description: sodium ion
    domain_of:
    - ontology class
    - entity